Analytical Report
C02533C1
Alerts
  • Summary
  • Square Bin
  • Cell Bin
  • Image
Spatial Gene Expression Distribution
Spatial gene expression distribution plot shows MID count at each spot (bin200)
Tissue Plot with Spot (bin200) Colored by MID Count
1,667,882,652
Total Reads
71,895
Mean MID per Bin200
8,182
Mean Gene Type per Bin200
135,184,151
Unique Reads
Key Metrices
Total Reads
Total number of sequenced reads
Valid CID Reads
Number of reads with CIDs matching the mask file and with MIDs passing QC
Invalid CID Reads
Number of reads with CIDs that cannot be matched with the mask file
Discarded MID Reads
Number of reads with MID that have been discarded since MID sequence quality does not satisfy with further analysis
Clean Reads
Number of Valid CID Reads that have passed QC
Non-Relevant Short Reads
Number of non-relevant short reads
Uniquely Mapped Reads
Number of reads that mapped uniquely to the reference genome
Multi-Mapped Reads
Number of reads that mapped more than one time on the genome
Unmapped Reads
Number of reads that cannot be mapped to the reference genome
Transcriptome
Number of reads that are aligned to transcripts of at least one gene
Unannotated Reads
Number of reads that cannot be aligned to transcript of one gene (intergenic)
Unique Reads
Number of reads in Transcriptome that have been corrected by MAPQ and deduplicated
Sequencing Saturation
Number of reads in Transcriptome that have been corrected by MAPQ with duplicated MID
Total Reads
100%
1,667,882,652
Valid CID Reads
81.0%
1,350,879,255
Clean Reads
88.6%
1,196,659,656
Uniquely Mapped Reads
75.9%
908,756,317
Transcriptome
89.5%
813,621,971
Unique Reads
16.6%
135,184,151
Sequencing Saturation
83.4%
678,437,820
Unannotated Reads
10.5%
95,134,346
Multi-Mapped Reads
19.4%
232,616,185
Unmapped Reads
4.6%
55,287,154
Non-Relevant Short Reads
11.4%
154,219,599
Invalid CID Reads
15.4%
256,484,063
Discarded MID Reads
3.6%
60,519,334
Information
Sequencing
Total Reads
Total number of sequenced reads
Total Q30
Ratio of bases with quality value exceeded 30 in the sequenced reads
CID Q30
Ratio of CID (Coordinate ID) bases with quality value exceeded 30
MID Q30
Ratio of MID (Molecule ID) bases with quality value exceeded 30
Total Reads
1,667,882,652
Total Q30
92.44%
CID Q30
89.6%
MID Q30
84.13%
Annotation
Exonic
Number of reads that mapped uniquely to an exonic region and on the same strand of the genome
Intronic
Number of reads that mapped uniquely to an intronic region and on the same strand of the genome
Intergenic
Number of reads that mapped uniquely to an intergenic region and on the same strand of the genome
Transcriptome
Number of reads that mapped to a unique gene in the transcriptome. These reads are considered for MID counting. (Transcriptome = Exonic + Intronic)
Antisense
Number of reads mapped to the transcriptome but on the opposite strand of their annotated gene
Exonic
780,161,468
Intronic
33,460,503
Intergenic
95,134,346
Transcriptome
813,621,971
Antisense
126,433,296
RNA Mapping
Clean Reads
Number of Valid CID Reads that have passed QC
Uniquely Mapped Reads
Number of reads that mapped uniquely to the reference genome
Multi-Mapped Reads
Number of reads that mapped more than one time on the genome
Unmapped Reads
Number of reads that cannot be mapped to the reference genome
Clean Reads
1,196,659,656
Uniquely Mapped Reads
908,756,317
Multi-Mapped Reads
232,616,185
Unmapped Reads
55,287,154
Tissue Segmentation
Tissue
DNB Under Tissue
Number of DNBs under tissue coverage region
mRNA-Captured DNBs Under Tissue
Number of DNBs under tissue that have captured mRNA
Genes Under Tissue
Number of detected gene under tissue coverage
Number of MID Under Tissue Coverage
Number of MID under tissue coverage
Fraction MID in Spots Under Tissue
Fraction of MID under tissue over total unique reads (MID Under Tissue / Unique Reads)
Reads Under Tissue
Number of reads with position prior to filtration under tissue coverage
Fraction Reads in Spots Under Tissue
Fraction of mapped reads under tissue over total mapped reads (Mapped Reads in Spots Under Tissue / (Valid CID Reads + Discarded MID Reads))
DNB Under Tissue
60,052,125
mRNA-Captured DNBs Under Tissue
33,787,671
Genes Under Tissue
25,633
Number of MID Under Tissue Coverage
115,176,890
Fraction MID in Spots Under Tissue
85.20%
Reads Under Tissue
1,165,272,042
Fraction Reads in Spots Under Tissue
82.56%
Sequencing Saturation
(left) Plot of the sequencing saturation as a function of sequencing depth(bin200)
(middle) Plot of the median number of genes detected per bin as a function of sequencing depth(bin200)
(right) Plot of the unique reads detected per bin as a function of sequencing depth(bin200)
Tissue Square Bin Statistics
Bin Size
The size of Bin which is the unit of aggregated DNBs in a squared region (i.e. Bin 50 = 50 * 50 DNBs)
Mean Reads (per bin)
Mean number of sequenced reads divided by the number of bins under tissue coverage
Median Reads (per bin)
Median number of sequenced reads divided by the number of bins under tissue coverage (pick the middle value after sorting)
Mean Gene Type (per bin)
Mean number of unique gene types divided by the number of bins under tissue coverage
Median Gene Type (per bin)
Median number of unique gene types divided by the number of bins under tissue coverage
Mean MID (per bin)
Mean number of MIDs divided by the number of bins under tissue coverage
Median MID (per bin)
Median number of MIDs divided by the number of bins under tissue coverage
Bin Size
Mean Reads
(per bin)
Median Reads
(per bin)
Mean Gene Type
(per bin)
Median Gene Type
(per bin)
Mean MID
(per bin)
Median MID
(per bin)
1
27.71
14
2.37
2
3.41
3
20
7,710
7,565
412
421
762
749
50
47,714
48,307
1,807
1,915
4,716
4,738
100
187,342
193,020
4,418
4,793
18,517
18,885
150
414,982
436,915
6,577
7,196
41,017
42,498
200
727,385
769,553
8,182
8,981
71,895
75,114
Bin 20
(left) Scatter plot of MID count and gene types in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene types in each bin
(bottom) Univariate distribution of MID count, gene types, and DNB numbers with rug along the x axis
Bin 50
(left) Scatter plot of MID count and gene types in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene types in each bin
(bottom) Univariate distribution of MID count, gene types, and DNB numbers with rug along the x axis
Bin 100
(left) Scatter plot of MID count and gene types in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene types in each bin
(bottom) Univariate distribution of MID count, gene types, and DNB numbers with rug along the x axis
Bin 150
(left) Scatter plot of MID count and gene types in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene types in each bin
(bottom) Univariate distribution of MID count, gene types, and DNB numbers with rug along the x axis
Bin 200
(left) Scatter plot of MID count and gene types in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene types in each bin
(bottom) Univariate distribution of MID count, gene types, and DNB numbers with rug along the x axis
Clustering
(left) Clustering spots (bin200) under tissue covered with the Leiden algorithm
(right) UMAP projections of spots (bin200) colored by automated clustering. Same color is assigned to spots that are within shorter distance and with similar gene expression profile
Tissue Plot with Spots (bin200)
UMAP Projection of Spots (bin200)
Cell Bin Statistics
Cell Count
Number of cells
Mean/Median Cell Area
Mean/Median cell area (pixel)
Mean/Median DNB Count
Mean/Median number of DNBs that have captured-mRNAs per cell
Mean/Median Gene Type
Mean/Median gene types per cell
Mean/Median MID
Mean/Median MID count per cell
Cell Count
110,976
Mean Cell Area
414
Median Cell Area
355
Mean DNB Count
242
Median DNB Count
204
Mean Gene Type
435
Median Gene Type
375
Mean MID
836
Median MID
655
Cell Bin
(left) Scatter plot of MID count and gene types in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene types in each bin
(bottom) Univariate distribution of MID count, gene types, DNB numbers, and cell area (pixel) with rug along the x axis
Clustering
(left) Clustering spots (cell bin) under tissue covered region with the Leiden algorithm
(right) UMAP projections of spots (cell bin) colored by automated clustering. Spots in the short distance are assigned with the same color have similar gene expression profile.
Tissue Plot with Spots (cell bin)
UMAP Projection of Spots (cellbin)
Image Information
Manufacture
motic
Model
Moticam Pro 500i
Scan Time
2023-7-17 16:30:0
Overlap
0.1
Exposure Time (ms)
0.439
Scan Rows
12
Scan Columns
11
FOV Height
2,032
FOV Width
2,428
Stain Type
HE
Stitched Image
No
Image Name
C02533C1_SC_20240131_165052_3.0.3
Stitching
Template Source Row No.
The row number of the template FOV used for predicting the entire template
Template Source Column No.
The column number of the template FOV used for predicting the entire template
Global Height
Height of the stitched image
Global Width
Width of the stitched image
Template Source Row No.
5
Template Source Column No.
1
Global Height
22,151
Global Width
24,288
QC
Image QC version
Image QC version
QC Pass
Whether the image(s) passed image QC quality check
Track Line Score
Reference score for track line detection
Clarity Score
Reference score for image clarity
Good FOV Count
Number of FOVs that have at least one track dot detected
Total FOV Count
Total number of FOVs
Stitching Score
Reference score for stitching
Tissue Segmentation Score
Reference score for tissue segmentation
Registration Score
Reference score for auto-aligning image with gene expression matrix
Image QC Version
3.0.3
QC Pass
Pass
Track Line Score
83
Clarity Score
-999
Good FOV Count
83
Total FOV Count
132
Stitching Score
97
Tissue Segmentation Score
100
Registration Score
99
Registration
ScaleX
The lateral scaling between image and template
ScaleY
The longitudinal scaling between image and template
Rotation
The rotation angle of the image relative to the template
Flip
Whether the image is flipped horizontally
Image X Offset
Offset between image and matrix in x direction
Image Y Offset
Offset between image and matrix in y direction
Counter Clockwise Rotation
Counter clockwise rotation angle
Manual ScaleX
The lateral scaling based on image center (manual-registration)
Manual ScaleY
The longitudinal scaling based on image center (manual-registration)
Manual Rotation
The rotation angle based on image center (manual-registration)
Matrix X Start
Gene expression matrix offset in x direction by DNB numbers
Matrix Y Start
Gene expression matrix offset in y direction by DNB numbers
Matrix Height
Gene expression matrix height
Matrix Width
Gene expression matrix width
ScaleX
0.996
ScaleY
0.997
Rotation
-0.385
Flip
True
Image X Offset
-316.49
Image Y Offset
4,108
Manual ScaleX
-
Manual ScaleY
-
Manual Rotation
-
Counter Clockwise Rotation
90
Matrix X Offset
0.00
Matrix Y Offset
0.00
Matrix Height
26,460
Matrix Width
26,460
Horizontal Image Stitching Deviation Heatmap
Image stitching deviation in the horizontal axis, a lighter color indicates better stitching (the heatmap and frame of axes have been adjusted with the registration parameters)
Vertical Image Stitching Deviation Heatmap
Image stitching deviation in the vertical axis, a lighter color indicates better stitching (the heatmap and frame of axes have been adjusted with the registration parameters)